Whitaker was ordained to the diaconate on July 15, 1863, and as an Episcopal priest on August 7, 1863. He was elected the first rector of St. Paul's Church, Englewood, Colorado in 1865 and technically remained there until March, 1867, although active as a missionary in the surrounding countryside. In 1863, Whitaker founded a small Episcopal congregation in Dayton, then in the Nevada Territory, a year after his wife helped found a Sunday School in Virginia City, Nevada. He became missionary bishop of Nevada and Arizona succeeding Joseph Cruikshank Talbot in 1869. Bishop Charles McIlvaine of Ohio, bishop Alfred Lee of Delaware and bishop Manton Eastburn of Massachusetts consecrated him on October 13, 1869. For many years, Bishop Whitaker made St. Paul's the Prospector Episcopal Church in Virginia City his base, and even rebuilt it after a disastrous fire in 1875. Rt.Rev. Whitaker also established in 1874 the Chapel of the Good Shepherd, a missionary church for Asian railroad workers in Carson City and the following year a chapel for Chinese workers in Virginia City. Growing anti-Chinese feeling also prompted its prime mover, Ah Foo, to become a missionary in China. Bishop Whitaker also established a mission to the Paiute tribe, St. James Mission in Wadsworth. Bishop Whitaker personally founded Trinity Church Mission in Reno in 1873, which somehow barely escaped the fire which destroyed much of the city in 1878. After securing a land grant from the Central Pacific Railroad, in 1879 he established Bishop Whitaker's School for Girls, a school for girls overlooking the Truckee River in Reno. However, in 1886 the University of Nevada established a free school nearby and its founder moved to Philadelphia, so the Episcopal school closed in 1894. Bishop Whitaker initially translated to the Diocese of Pennsylvania to serve as coadjutor to bishop William B. Stevens, and stopped overseeing the Nevada diocese in 1888, after the General Convention transferred oversight to bishop Abiel Leonard of Salt Lake City and a year after Bishop Whitaker succeeded Bishop Stevens as diocesan bishop of Pennsylvania. He served as the diocese's fifth bishop from 1887-1911. From 1904 until his death, he also led the Pennsylvania Bible Society as its 10th president. Beginning in 1902, his eventual successor, Alexander Mackay-Smith served as his coadjutor.
Death and legacy
The elderly bishop died in Philadelphia after contracting influenza, and the funeral was held at the Church of Our Savior. Although the Episcopal school Rev. Whitaker founded in Reno closed in 1894 and its buildings were used first by the University of Nevada and later as a hospital, the site is now a park named after its founding missionary bishop. The University of Arizona has some of his papers, as do Yale and the University of Michigan in their Protestant Episcopal bishops collections.